Outcomes:
Ancestry data:
Association analysis
Multi-trait association analysis
0.05 / 229384
[1] 2.179751e-07
Table of top SNP and other SNPs from the same ancestry segment (chr11acs76906):
| snp | zscore | pval | chr | pos | acs | num_snps | size | trait |
|---|---|---|---|---|---|---|---|---|
| rs933920 | 2.928 | 0.003413 | 11 | 12481110 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs4756884 | -2.557 | 0.01055 | 11 | 12474098 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs4756866 | -2.369 | 0.01781 | 11 | 12448846 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs10831815 | 2.076 | 0.03792 | 11 | 12446924 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs10741590 | 2.056 | 0.03976 | 11 | 12463318 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs1344615 | -1.901 | 0.05725 | 11 | 12454046 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs11022358 | 1.647 | 0.09951 | 11 | 12470449 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs10831827 | -1.603 | 0.1089 | 11 | 12483197 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs1365403 | 1.571 | 0.1161 | 11 | 12476231 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
| rs1346220 | 1.543 | 0.1229 | 11 | 12480087 | chr11acs76906 | 21 | 36273 | FEV1pp_utah |
NCBI quiery (the latest dbSNP build and latest reference genome):
| Query | Chromosome | Marker | Class | Gene | Alleles | Major | Minor | MAF | BP | AncestralAllele |
|---|---|---|---|---|---|---|---|---|---|---|
| rs933920 | 11 | rs933920 | snp | PARVA | A/G | A | G | 0.0377 | 12459563 | A,A,A,A,A,A |
| rs4756884 | 11 | rs4756884 | snp | PARVA | A/G | A | G | 0.3768 | 12452551 | A,A,A,A,A |
| rs4756866 | 11 | rs4756866 | snp | PARVA | A/G | A | G | 0.031 | 12427299 | A,A,A,A,A,A |
| rs10831815 | 11 | rs10831815 | snp | PARVA | A/C | C | A | 0.4018 | 12425377 | C,C,C,C,C,C |
| rs10741590 | 11 | rs10741590 | snp | PARVA | C/T | C | T | 0.1791 | 12441771 | C,C,C,C,C,C |
| rs1344615 | 11 | rs1344615 | snp | PARVA | C/T | C | T | 0.1214 | 12432499 | C,C,C,C,C,C |
| rs11022358 | 11 | rs11022358 | snp | PARVA | C/T | T | C | 0.2612 | 12448902 | C,C,C,C,C,C |
| rs10831827 | 11 | rs10831827 | snp | PARVA | A/G | G | A | 0.2586 | 12461650 | G,G,G,G,G,G |
| rs1365403 | 11 | rs1365403 | snp | PARVA | G/T | G | T | 0.0859 | 12454684 | T,T,T,T,T,T |
| rs1346220 | 11 | rs1346220 | snp | PARVA | C/T | C | T | 0.0617 | 12458540 | T,T,T,T,T,T |
All MeSH Categories
Diseases Category
Respiratory Tract Diseases
Lung Diseases
Lung Diseases, Obstructive
Pulmonary Disease, Chronic Obstructive
Obstructive Sleep Apnea; Mesh Term
Categorization 1:
All MeSH Categories
Diseases Category
Respiratory Tract Diseases
Respiration Disorders
Apnea
Sleep Apnea Syndromes
Sleep Apnea, Obstructive
Categorization 2:
All MeSH Categories
Diseases Category
Nervous System Diseases
Sleep Wake Disorders
Dyssomnias
Sleep Disorders, Intrinsic
Sleep Apnea Syndromes
Sleep Apnea, Obstructive
| trait | ver | formula |
|---|---|---|
| FEV1pp_utah | 9 | imp_FEV1pp_utah ~ Age_Enroll + gender + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigarNow + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) |
| FEV1_utah | 9 | imp_FEV1_utah ~ Age_Enroll + Age_Enroll2 + gender + Height_CM + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigarNow + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) |
| FVCpp_utah | 9 | imp_FVCpp_utah ~ Age_Enroll + gender + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigarNow + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) |
| FVC_utah | 9 | imp_FVC_utah ~ Age_Enroll + Age_Enroll2 + gender + Height_CM + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigarNow + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) |
| FEV1_FVC_utah | 9 | imp_FEV1_FVC_utah ~ Age_Enroll + Age_Enroll2 + gender + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) |
| log_pctEmph_Slicer | 9 | imp_log_pctEmph_Slicer ~ Age_Enroll + gender + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigarNow + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) + (1|scanner_gr) |
| TLCpp_race_adjusted | 9 | imp_TLCpp_race_adjusted ~ Age_Enroll + gender + Duration_Smoking + log_CigPerDaySmokAvg + SmokCigarNow + SmokCigNow + SmokCigNow0_15 + acs_global2 + (0 + dummy(SmokCigNow0_15Rev)|rsid1) + (0 + dummy(SmokCigNowRev)|rsid2) + (1|ccenter) |
| Test | Statistics | Distribution | Reference |
|---|---|---|---|
| Omnibus | \(z^T \Sigma^{-1} z\) | \(\chi^2(p)\) | (Aschard et al., in preparation) |
| sumZ | \((1^T z)^2 / 1^T \Sigma^{-1} 1\) | \(\chi^2(1)\) | (Province et al, 2013) |
jtab <- switch(method,
"omnibus" = {
P1 <- tcrossprod(Z, Sigma_inv)
P2 <- P1 * Z # element-wise multiplication
z2score <- rowSums(P2)
data_frame(z2score = z2score) %>%
mutate(pval = pchisq(z2score, df = ncol(Z), lower = FALSE))
},
"metacp" = {
P1 <- tcrossprod(Z, Sigma_inv)
z2score <- (rowSums(P1))^2 / sum(Sigma_inv)
data_frame(z2score = z2score) %>%
mutate(pval = pchisq(z2score, df = 1, lower = FALSE))
},
"sum2" = {
z2score <- (rowSums(Z))^2 / sum(Sigma)
data_frame(z2score = z2score) %>%
mutate(pval = pchisq(z2score, df = 1, lower = FALSE))
},
stop("switch"))